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Author SHA1 Message Date
Ricardo Wurmus
9b270ccefa
gnu: r-abn: Update to 3.0.3. 
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.3.

Change-Id: Id94ec47d805af9da63dbf43a9edbd5e7c3a5a62a
 2023-11-15 15:55:20 +01:00
Ricardo Wurmus
fefc250c60
gnu: r-activepathways: Update to 2.0.3. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.3.

Change-Id: I4199c307d48583c0894a39af78f6a4027cb0cf54
 2023-11-15 15:55:20 +01:00
Ricardo Wurmus
285dd08443
gnu: r-ggpicrust2: Update to 1.7.3. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.3.

Change-Id: I18ab123d640ceec9315a21dff48ed2f1ea4ddff5
 2023-11-15 15:55:20 +01:00
Mădălin Ionel Patrașcu
a0d337e79c
gnu: Add r-bcrank. 
* gnu/packages/bioconductor.scm (r-bcrank): New variable.

Change-Id: Id43ae3b7f6eff54e1180b489c90fc72176751f9f
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
08c745dcfc
gnu: Add r-bbcanalyzer. 
* gnu/packages/bioconductor.scm (r-bbcanalyzer): New variable.

Change-Id: Icd3c77c9522d73638ddb0934ad332ddb7b947a8e
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
17978740e5
gnu: Add r-baynorm. 
* gnu/packages/bioconductor.scm (r-baynorm): New variable.

Change-Id: I83e82d3d0362874918f423ab01f038c74f3eb265
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
53b4e01e29
gnu: Add r-bayesspace. 
* gnu/packages/bioconductor.scm (r-bayesspace): New variable.

Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab
 2023-11-13 15:03:29 +01:00
Mădălin Ionel Patrașcu
598b911334
gnu: Add r-bayesknockdown. 
* gnu/packages/bioconductor.scm (r-bayesknockdown): New variable.

Change-Id: Icceffc04071efaa8a8b79144005fa7745abc7e1a
 2023-11-13 15:01:15 +01:00
Mădălin Ionel Patrașcu
77025bd511
gnu: Add r-basicstarrseq. 
* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable.

Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
 2023-11-13 15:00:48 +01:00
Mădălin Ionel Patrașcu
4e1c6f4998
gnu: Add r-basics. 
* gnu/packages/bioconductor.scm (r-basics): New variable.

Change-Id: I6f0afeeb41f667d780707af65034d5ba978f0d4a
 2023-11-13 15:00:00 +01:00
Mădălin Ionel Patrașcu
47a4195649
gnu: Add r-basic4cseq. 
* gnu/packages/bioconductor.scm (r-basic4cseq): New variable.

Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3
 2023-11-13 14:59:26 +01:00
Mădălin Ionel Patrașcu
459d9ebd2a
gnu: Add r-bsgenome-ecoli-ncbi-20080805. 
* gnu/packages/bioconductor.scm (r-bsgenome-ecoli-ncbi-20080805):
    New variable.

Change-Id: Ic42527fa334be4c23ebe2e19461571d899db77ca
 2023-11-13 14:57:00 +01:00
Mădălin Ionel Patrașcu
628926de80
gnu: Add r-bags. 
* gnu/packages/bioconductor.scm (r-bags): New variable.

Change-Id: If0c533898a5e05809f23e7e8b52fc3d5fbffc8fb
 2023-11-13 14:55:55 +01:00
Mădălin Ionel Patrașcu
d0251c23b9
gnu: Add r-breastcancervdx. 
* gnu/packages/bioconductor.scm (r-breastcancervdx): New variable.

Change-Id: Ia3437ab67a00ce23c61553ff15f940b8a3ee9c8a
 2023-11-13 14:55:55 +01:00
Mădălin Ionel Patrașcu
adf716c171
gnu: Add r-screpertoire. 
* gnu/packages/bioconductor.scm (r-screpertoire): New variable.

Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
01b7d917a2
gnu: Add r-powertcr. 
* gnu/packages/bioconductor.scm (r-powertcr): New variable.

Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
58786c82df
gnu: Add r-rnbeads. 
* gnu/packages/bioconductor.scm (r-rnbeads): New variable.

Change-Id: I78b248a449473fc37ac414295faa6e61269b8625
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 17:09:53 +01:00
Mădălin Ionel Patrașcu
cb0e60cccf
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked. 
* gnu/packages/bioconductor.scm
  (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.

Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
 2023-11-04 16:30:11 +01:00
Mădălin Ionel Patrașcu
7eeab6417f
gnu: Add r-methylaid. 
* gnu/packages/bioconductor.scm (r-methylaid): New variable.

Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 11:37:15 +01:00
Ricardo Wurmus
8be2f44765
gnu: Remove r-sigpathway. 
This package has been removed with the release of Bioconductor 3.18.

* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.

Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
38b5777ec8
gnu: r-rhdf5filters: Simplify. 
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.

Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
142313cf0c
gnu: Remove r-genomegraphs. 
This package had been removed from Bioconductor with release 3.11.

* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.

Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
0150529188
gnu: Remove r-wavetiling. 
This package had been removed from Bioconductor since release 3.12.

* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.

Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
abaca151b2
gnu: r-mpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add MPO.sqlite.

Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add HPO.sqlite.

Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
a938342899
gnu: r-rhdf5lib: Adjust modifications to Makevars. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch.

Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
c82c9c8090
gnu: r-phyloseq: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0.

Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
1c3e8ab395
gnu: r-tximeta: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0.

Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
270d7e1079
gnu: r-tricycle: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0.

Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
9ee38f4ee6
gnu: r-tcgabiolinks: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0.

Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
28480926a5
gnu: r-biscuiteer: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0.

Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
53ebbff56c
gnu: r-omnipathr: Update to 3.10.1. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1.
[propagated-inputs]: Add r-lubridate and r-stringi.

Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
41a4f01473
gnu: r-omicade4: Update to 1.42.0. 
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0.

Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
73efb254d8
gnu: r-dmrseq: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.22.0.

Change-Id: I738c2fb7e0fa3e816d3767f854b8f9ed77425591
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
f6e56299e7
gnu: r-dada2: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.30.0.

Change-Id: I0955c3a61b4d81cd6809e2eb287d8acfcccfb789
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
407e9b2710
gnu: r-bsseq: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.38.0.

Change-Id: Ie31f0b5c726da98a0caa4c658a5c62c1a5f40eaa
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
69d7d7a6db
gnu: r-biotmle: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.26.0.

Change-Id: Ied1d1e649fba277aa724040af31334f664d2debd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
9f2c8b711b
gnu: r-biotip: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.16.0.

Change-Id: I73503554b0271e5fe950c6da367b4893972f27e9
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
a7d1b8832a
gnu: r-bioqc: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.30.0.

Change-Id: I0b5fd7cac1283a7f12a1221ad453eb56767e8b90
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
ee259a9ad9
gnu: r-bionetstat: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.22.0.

Change-Id: I92f2ebef0b65b947a719bdd1008f07ce279263a4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
b0190a7d5c
gnu: r-bionet: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.62.0.

Change-Id: I0712a4ba67c27b32d6666e91d9515f0299e61848
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
63f3a845ea
gnu: r-bionero: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.10.0.

Change-Id: I396a37dd28571a471b45d4d8aca6ce40a1cbd384
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
4ccceb31b9
gnu: r-biomvcclass: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.70.0.

Change-Id: I0c6214669ec284d314eb7dc90270558934070e4b
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b4e803a8a9
gnu: r-mvcclass: Update to 1.76.0. 
* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.76.0.

Change-Id: I6e7fa851c804009ae41a955b117d95b33fd1b2f0
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
c91a1a8bc8
gnu: r-biomformat: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.30.0.

Change-Id: I661d11f81a0dedbc8381b5ba1806643b5ff52aa6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
2b4dcd4a7b
gnu: r-biodb: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.10.0.

Change-Id: If1d14855b2bf134741c54c0a51daefdf2b80a49f
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
9480ea5046
gnu: r-biocthis: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.12.0.

Change-Id: I8400ebfd178f916488e022152e75db59f05994e6
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
327c9bd7c8
gnu: r-basilisk: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.14.0.

Change-Id: I86f5306de138eb1fedffbae65c14f9acd504c86c
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b5527cc3c6
gnu: r-basilisk-utils: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.14.0.

Change-Id: I6113042a10770ee50e4ef997ee41fe109f917885
 2023-11-03 22:49:27 +01:00
Ricardo Wurmus
b2389dcfc1
gnu: r-dir-expiry: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.10.0.

Change-Id: I1081ec981a52a51a351d98e5079f8fd4bcc399d0
 2023-11-03 22:49:27 +01:00